I managed to reproduce the bug with another character I rushed through on Story mode. Basically, what happened is that I killed Mokeha in Satahuzi, which prompted the Storm Speaker to attack me, but I didn't kill her, I sneaked past her. Which means she couldn't be on the beach, but I'm also thinking since I didn't kill her, any failsaves about the ship relating to her death don't trigger. I'm going to try to kill her with my main character to see if this will jolt the proper triggers.
EDIT: When I killed her, the NPC which is supposed to spawn instead of her spawns and I can continue. Maybe look into her spawning if the Storm Speaker is hostile and not only dead for a later patch or something.
Christliar's post in Game breaking bug in Vilario's Rest was marked as the answer